12 |
|
#include "mpiSimulation.hpp" |
13 |
|
#endif |
14 |
|
|
15 |
+ |
// some defines for ensemble and Forcefield cases |
16 |
+ |
|
17 |
+ |
#define NVE_ENS 0 |
18 |
+ |
#define NVT_ENS 1 |
19 |
+ |
#define NPTi_ENS 2 |
20 |
+ |
#define NPTf_ENS 3 |
21 |
+ |
#define NPTim_ENS 4 |
22 |
+ |
#define NPTfm_ENS 5 |
23 |
+ |
|
24 |
+ |
|
25 |
+ |
#define FF_DUFF 0 |
26 |
+ |
#define FF_LJ 1 |
27 |
+ |
|
28 |
+ |
|
29 |
|
SimSetup::SimSetup(){ |
30 |
|
stamps = new MakeStamps(); |
31 |
|
globals = new Globals(); |
78 |
|
|
79 |
|
void SimSetup::createSim( void ){ |
80 |
|
|
81 |
< |
MakeStamps *the_stamps; |
68 |
< |
Globals* the_globals; |
69 |
< |
int i, j; |
70 |
< |
|
71 |
< |
// get the stamps and globals; |
72 |
< |
the_stamps = stamps; |
73 |
< |
the_globals = globals; |
74 |
< |
|
75 |
< |
// set the easy ones first |
76 |
< |
simnfo->target_temp = the_globals->getTargetTemp(); |
77 |
< |
simnfo->dt = the_globals->getDt(); |
78 |
< |
simnfo->run_time = the_globals->getRunTime(); |
79 |
< |
|
80 |
< |
// get the ones we know are there, yet still may need some work. |
81 |
< |
n_components = the_globals->getNComponents(); |
82 |
< |
strcpy( force_field, the_globals->getForceField() ); |
83 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
< |
strcpy( simnfo->ensemble, ensemble ); |
85 |
< |
|
86 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 |
< |
simnfo->usePBC = the_globals->getPBC(); |
88 |
< |
|
89 |
< |
|
90 |
< |
|
91 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 |
< |
else{ |
94 |
< |
sprintf( painCave.errMsg, |
95 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
96 |
< |
force_field ); |
97 |
< |
painCave.isFatal = 1; |
98 |
< |
simError(); |
99 |
< |
} |
100 |
< |
|
101 |
< |
#ifdef IS_MPI |
102 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
103 |
< |
MPIcheckPoint(); |
104 |
< |
#endif // is_mpi |
105 |
< |
|
81 |
> |
int i, j, k, globalAtomIndex; |
82 |
|
|
83 |
< |
|
108 |
< |
// get the components and calculate the tot_nMol and indvidual n_mol |
109 |
< |
the_components = the_globals->getComponents(); |
110 |
< |
components_nmol = new int[n_components]; |
111 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
112 |
< |
|
113 |
< |
if( !the_globals->haveNMol() ){ |
114 |
< |
// we don't have the total number of molecules, so we assume it is |
115 |
< |
// given in each component |
116 |
< |
|
117 |
< |
tot_nmol = 0; |
118 |
< |
for( i=0; i<n_components; i++ ){ |
119 |
< |
|
120 |
< |
if( !the_components[i]->haveNMol() ){ |
121 |
< |
// we have a problem |
122 |
< |
sprintf( painCave.errMsg, |
123 |
< |
"SimSetup Error. No global NMol or component NMol" |
124 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
125 |
< |
painCave.isFatal = 1; |
126 |
< |
simError(); |
127 |
< |
} |
128 |
< |
|
129 |
< |
tot_nmol += the_components[i]->getNMol(); |
130 |
< |
components_nmol[i] = the_components[i]->getNMol(); |
131 |
< |
} |
132 |
< |
} |
133 |
< |
else{ |
134 |
< |
sprintf( painCave.errMsg, |
135 |
< |
"SimSetup error.\n" |
136 |
< |
"\tSorry, the ability to specify total" |
137 |
< |
" nMols and then give molfractions in the components\n" |
138 |
< |
"\tis not currently supported." |
139 |
< |
" Please give nMol in the components.\n" ); |
140 |
< |
painCave.isFatal = 1; |
141 |
< |
simError(); |
142 |
< |
|
143 |
< |
|
144 |
< |
// tot_nmol = the_globals->getNMol(); |
145 |
< |
|
146 |
< |
// //we have the total number of molecules, now we check for molfractions |
147 |
< |
// for( i=0; i<n_components; i++ ){ |
148 |
< |
|
149 |
< |
// if( !the_components[i]->haveMolFraction() ){ |
150 |
< |
|
151 |
< |
// if( !the_components[i]->haveNMol() ){ |
152 |
< |
// //we have a problem |
153 |
< |
// std::cerr << "SimSetup error. Neither molFraction nor " |
154 |
< |
// << " nMol was given in component |
155 |
< |
|
156 |
< |
} |
157 |
< |
|
158 |
< |
#ifdef IS_MPI |
159 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
160 |
< |
MPIcheckPoint(); |
161 |
< |
#endif // is_mpi |
162 |
< |
|
163 |
< |
// make an array of molecule stamps that match the components used. |
164 |
< |
// also extract the used stamps out into a separate linked list |
165 |
< |
|
166 |
< |
simnfo->nComponents = n_components; |
167 |
< |
simnfo->componentsNmol = components_nmol; |
168 |
< |
simnfo->compStamps = comp_stamps; |
169 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
83 |
> |
// gather all of the information from the Bass file |
84 |
|
|
85 |
< |
char* id; |
172 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
173 |
< |
LinkedMolStamp* currentStamp = NULL; |
174 |
< |
for( i=0; i<n_components; i++ ){ |
85 |
> |
gatherInfo(); |
86 |
|
|
87 |
< |
id = the_components[i]->getType(); |
177 |
< |
comp_stamps[i] = NULL; |
178 |
< |
|
179 |
< |
// check to make sure the component isn't already in the list |
87 |
> |
// creation of complex system objects |
88 |
|
|
89 |
< |
comp_stamps[i] = headStamp->match( id ); |
182 |
< |
if( comp_stamps[i] == NULL ){ |
183 |
< |
|
184 |
< |
// extract the component from the list; |
185 |
< |
|
186 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
187 |
< |
if( currentStamp == NULL ){ |
188 |
< |
sprintf( painCave.errMsg, |
189 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
190 |
< |
"list of declared molecules\n", |
191 |
< |
id ); |
192 |
< |
painCave.isFatal = 1; |
193 |
< |
simError(); |
194 |
< |
} |
195 |
< |
|
196 |
< |
headStamp->add( currentStamp ); |
197 |
< |
comp_stamps[i] = headStamp->match( id ); |
198 |
< |
} |
199 |
< |
} |
89 |
> |
sysObjectsCreation(); |
90 |
|
|
91 |
< |
#ifdef IS_MPI |
202 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
203 |
< |
MPIcheckPoint(); |
204 |
< |
#endif // is_mpi |
91 |
> |
// check on the post processing info |
92 |
|
|
93 |
+ |
finalInfoCheck(); |
94 |
|
|
95 |
+ |
// initialize the system coordinates |
96 |
|
|
97 |
< |
|
209 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
210 |
< |
|
211 |
< |
tot_atoms = 0; |
212 |
< |
tot_bonds = 0; |
213 |
< |
tot_bends = 0; |
214 |
< |
tot_torsions = 0; |
215 |
< |
for( i=0; i<n_components; i++ ){ |
216 |
< |
|
217 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
221 |
< |
} |
222 |
< |
|
223 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
224 |
< |
|
225 |
< |
simnfo->n_atoms = tot_atoms; |
226 |
< |
simnfo->n_bonds = tot_bonds; |
227 |
< |
simnfo->n_bends = tot_bends; |
228 |
< |
simnfo->n_torsions = tot_torsions; |
229 |
< |
simnfo->n_SRI = tot_SRI; |
230 |
< |
simnfo->n_mol = tot_nmol; |
231 |
< |
|
97 |
> |
initSystemCoords(); |
98 |
|
|
233 |
– |
#ifdef IS_MPI |
99 |
|
|
100 |
< |
// divide the molecules among processors here. |
236 |
< |
|
237 |
< |
mpiSim = new mpiSimulation( simnfo ); |
238 |
< |
|
239 |
< |
|
100 |
> |
// make the output filenames |
101 |
|
|
102 |
< |
globalIndex = mpiSim->divideLabor(); |
103 |
< |
|
104 |
< |
|
244 |
< |
|
245 |
< |
// set up the local variables |
102 |
> |
makeOutNames(); |
103 |
> |
|
104 |
> |
// make the integrator |
105 |
|
|
106 |
< |
int localMol, allMol; |
248 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
249 |
< |
|
250 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
251 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
252 |
< |
|
253 |
< |
allMol = 0; |
254 |
< |
localMol = 0; |
255 |
< |
local_atoms = 0; |
256 |
< |
local_bonds = 0; |
257 |
< |
local_bends = 0; |
258 |
< |
local_torsions = 0; |
259 |
< |
for( i=0; i<n_components; i++ ){ |
260 |
< |
|
261 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
262 |
< |
|
263 |
< |
if( mol2proc[j] == worldRank ){ |
264 |
< |
|
265 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
266 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
267 |
< |
local_bends += comp_stamps[i]->getNBends(); |
268 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
269 |
< |
localMol++; |
270 |
< |
} |
271 |
< |
allMol++; |
272 |
< |
} |
273 |
< |
} |
274 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
106 |
> |
makeIntegrator(); |
107 |
|
|
276 |
– |
|
277 |
– |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
278 |
– |
|
279 |
– |
if( local_atoms != simnfo->n_atoms ){ |
280 |
– |
sprintf( painCave.errMsg, |
281 |
– |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 |
– |
" localAtom (%d) are not equal.\n", |
283 |
– |
simnfo->n_atoms, |
284 |
– |
local_atoms ); |
285 |
– |
painCave.isFatal = 1; |
286 |
– |
simError(); |
287 |
– |
} |
288 |
– |
|
289 |
– |
simnfo->n_bonds = local_bonds; |
290 |
– |
simnfo->n_bends = local_bends; |
291 |
– |
simnfo->n_torsions = local_torsions; |
292 |
– |
simnfo->n_SRI = local_SRI; |
293 |
– |
simnfo->n_mol = localMol; |
294 |
– |
|
295 |
– |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
296 |
– |
MPIcheckPoint(); |
297 |
– |
|
298 |
– |
|
299 |
– |
#endif // is_mpi |
300 |
– |
|
301 |
– |
|
302 |
– |
// create the atom and short range interaction arrays |
303 |
– |
|
304 |
– |
Atom::createArrays(simnfo->n_atoms); |
305 |
– |
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
– |
the_molecules = new Molecule[simnfo->n_mol]; |
307 |
– |
int molIndex; |
308 |
– |
|
309 |
– |
// initialize the molecule's stampID's |
310 |
– |
|
108 |
|
#ifdef IS_MPI |
109 |
< |
|
109 |
> |
mpiSim->mpiRefresh(); |
110 |
> |
#endif |
111 |
|
|
112 |
< |
molIndex = 0; |
315 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 |
< |
|
317 |
< |
if(mol2proc[i] == worldRank ){ |
318 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
319 |
< |
molIndex++; |
320 |
< |
} |
321 |
< |
} |
112 |
> |
// initialize the Fortran |
113 |
|
|
114 |
< |
#else // is_mpi |
324 |
< |
|
325 |
< |
molIndex = 0; |
326 |
< |
for(i=0; i<n_components; i++){ |
327 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
328 |
< |
the_molecules[molIndex].setStampID( i ); |
329 |
< |
molIndex++; |
330 |
< |
} |
331 |
< |
} |
332 |
< |
|
333 |
< |
|
334 |
< |
#endif // is_mpi |
335 |
< |
|
336 |
< |
|
337 |
< |
if( simnfo->n_SRI ){ |
338 |
< |
|
339 |
< |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 |
< |
|
341 |
< |
Exclude::createArray(simnfo->n_SRI); |
342 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
343 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
344 |
< |
simnfo->globalExcludes = new int; |
345 |
< |
simnfo->n_exclude = tot_SRI; |
346 |
< |
} |
347 |
< |
else{ |
348 |
< |
|
349 |
< |
Exclude::createArray( 1 ); |
350 |
< |
the_excludes = new Exclude*; |
351 |
< |
the_excludes[0] = new Exclude(0); |
352 |
< |
the_excludes[0]->setPair( 0,0 ); |
353 |
< |
simnfo->globalExcludes = new int; |
354 |
< |
simnfo->globalExcludes[0] = 0; |
355 |
< |
simnfo->n_exclude = 0; |
356 |
< |
} |
357 |
< |
|
358 |
< |
// set the arrays into the SimInfo object |
359 |
< |
|
360 |
< |
simnfo->atoms = the_atoms; |
361 |
< |
simnfo->molecules = the_molecules; |
362 |
< |
simnfo->nGlobalExcludes = 0; |
363 |
< |
simnfo->excludes = the_excludes; |
364 |
< |
|
365 |
< |
|
366 |
< |
// get some of the tricky things that may still be in the globals |
367 |
< |
|
368 |
< |
|
369 |
< |
if( the_globals->haveBox() ){ |
370 |
< |
simnfo->box_x = the_globals->getBox(); |
371 |
< |
simnfo->box_y = the_globals->getBox(); |
372 |
< |
simnfo->box_z = the_globals->getBox(); |
373 |
< |
} |
374 |
< |
else if( the_globals->haveDensity() ){ |
375 |
< |
|
376 |
< |
double vol; |
377 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
378 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
379 |
< |
simnfo->box_y = simnfo->box_x; |
380 |
< |
simnfo->box_z = simnfo->box_x; |
381 |
< |
} |
382 |
< |
else{ |
383 |
< |
if( !the_globals->haveBoxX() ){ |
384 |
< |
sprintf( painCave.errMsg, |
385 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
386 |
< |
painCave.isFatal = 1; |
387 |
< |
simError(); |
388 |
< |
} |
389 |
< |
simnfo->box_x = the_globals->getBoxX(); |
390 |
< |
|
391 |
< |
if( !the_globals->haveBoxY() ){ |
392 |
< |
sprintf( painCave.errMsg, |
393 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
394 |
< |
painCave.isFatal = 1; |
395 |
< |
simError(); |
396 |
< |
} |
397 |
< |
simnfo->box_y = the_globals->getBoxY(); |
398 |
< |
|
399 |
< |
if( !the_globals->haveBoxZ() ){ |
400 |
< |
sprintf( painCave.errMsg, |
401 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
402 |
< |
painCave.isFatal = 1; |
403 |
< |
simError(); |
404 |
< |
} |
405 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
406 |
< |
} |
407 |
< |
|
408 |
< |
#ifdef IS_MPI |
409 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
410 |
< |
MPIcheckPoint(); |
411 |
< |
#endif // is_mpi |
412 |
< |
|
413 |
< |
|
414 |
< |
// initialize the arrays |
415 |
< |
|
416 |
< |
the_ff->setSimInfo( simnfo ); |
417 |
< |
|
418 |
< |
makeMolecules(); |
419 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
420 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
421 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
422 |
< |
} |
423 |
< |
|
424 |
< |
if (the_globals->getUseRF() ) { |
425 |
< |
simnfo->useReactionField = 1; |
426 |
< |
|
427 |
< |
if( !the_globals->haveECR() ){ |
428 |
< |
sprintf( painCave.errMsg, |
429 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
430 |
< |
"box length for the electrostaticCutoffRadius.\n" |
431 |
< |
"I hope you have a very fast processor!\n"); |
432 |
< |
painCave.isFatal = 0; |
433 |
< |
simError(); |
434 |
< |
double smallest; |
435 |
< |
smallest = simnfo->box_x; |
436 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
437 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
438 |
< |
simnfo->ecr = 0.5 * smallest; |
439 |
< |
} else { |
440 |
< |
simnfo->ecr = the_globals->getECR(); |
441 |
< |
} |
442 |
< |
|
443 |
< |
if( !the_globals->haveEST() ){ |
444 |
< |
sprintf( painCave.errMsg, |
445 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
446 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
447 |
< |
); |
448 |
< |
painCave.isFatal = 0; |
449 |
< |
simError(); |
450 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
451 |
< |
} else { |
452 |
< |
simnfo->est = the_globals->getEST(); |
453 |
< |
} |
454 |
< |
|
455 |
< |
if(!the_globals->haveDielectric() ){ |
456 |
< |
sprintf( painCave.errMsg, |
457 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
458 |
< |
"setting a dielectric constant!\n" |
459 |
< |
); |
460 |
< |
painCave.isFatal = 1; |
461 |
< |
simError(); |
462 |
< |
} |
463 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
464 |
< |
} else { |
465 |
< |
if (simnfo->n_dipoles) { |
466 |
< |
|
467 |
< |
if( !the_globals->haveECR() ){ |
468 |
< |
sprintf( painCave.errMsg, |
469 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
470 |
< |
"box length for the electrostaticCutoffRadius.\n" |
471 |
< |
"I hope you have a very fast processor!\n"); |
472 |
< |
painCave.isFatal = 0; |
473 |
< |
simError(); |
474 |
< |
double smallest; |
475 |
< |
smallest = simnfo->box_x; |
476 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
477 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
478 |
< |
simnfo->ecr = 0.5 * smallest; |
479 |
< |
} else { |
480 |
< |
simnfo->ecr = the_globals->getECR(); |
481 |
< |
} |
482 |
< |
|
483 |
< |
if( !the_globals->haveEST() ){ |
484 |
< |
sprintf( painCave.errMsg, |
485 |
< |
"SimSetup Warning: using default value of 5% of the" |
486 |
< |
"electrostaticCutoffRadius for the " |
487 |
< |
"electrostaticSkinThickness\n" |
488 |
< |
); |
489 |
< |
painCave.isFatal = 0; |
490 |
< |
simError(); |
491 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
492 |
< |
} else { |
493 |
< |
simnfo->est = the_globals->getEST(); |
494 |
< |
} |
495 |
< |
} |
496 |
< |
} |
114 |
> |
initFortran(); |
115 |
|
|
498 |
– |
#ifdef IS_MPI |
499 |
– |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
500 |
– |
MPIcheckPoint(); |
501 |
– |
#endif // is_mpi |
116 |
|
|
503 |
– |
if( the_globals->haveInitialConfig() ){ |
504 |
– |
|
505 |
– |
InitializeFromFile* fileInit; |
506 |
– |
#ifdef IS_MPI // is_mpi |
507 |
– |
if( worldRank == 0 ){ |
508 |
– |
#endif //is_mpi |
509 |
– |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
510 |
– |
#ifdef IS_MPI |
511 |
– |
}else fileInit = new InitializeFromFile( NULL ); |
512 |
– |
#endif |
513 |
– |
fileInit->read_xyz( simnfo ); // default velocities on |
117 |
|
|
515 |
– |
delete fileInit; |
516 |
– |
} |
517 |
– |
else{ |
518 |
– |
|
519 |
– |
#ifdef IS_MPI |
520 |
– |
|
521 |
– |
// no init from bass |
522 |
– |
|
523 |
– |
sprintf( painCave.errMsg, |
524 |
– |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
525 |
– |
painCave.isFatal; |
526 |
– |
simError(); |
527 |
– |
|
528 |
– |
#else |
529 |
– |
|
530 |
– |
initFromBass(); |
531 |
– |
|
532 |
– |
|
533 |
– |
#endif |
534 |
– |
} |
535 |
– |
|
536 |
– |
#ifdef IS_MPI |
537 |
– |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
538 |
– |
MPIcheckPoint(); |
539 |
– |
#endif // is_mpi |
540 |
– |
|
541 |
– |
|
542 |
– |
|
543 |
– |
|
544 |
– |
|
545 |
– |
|
546 |
– |
|
547 |
– |
#ifdef IS_MPI |
548 |
– |
if( worldRank == 0 ){ |
549 |
– |
#endif // is_mpi |
550 |
– |
|
551 |
– |
if( the_globals->haveFinalConfig() ){ |
552 |
– |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
553 |
– |
} |
554 |
– |
else{ |
555 |
– |
strcpy( simnfo->finalName, inFileName ); |
556 |
– |
char* endTest; |
557 |
– |
int nameLength = strlen( simnfo->finalName ); |
558 |
– |
endTest = &(simnfo->finalName[nameLength - 5]); |
559 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
560 |
– |
strcpy( endTest, ".eor" ); |
561 |
– |
} |
562 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
563 |
– |
strcpy( endTest, ".eor" ); |
564 |
– |
} |
565 |
– |
else{ |
566 |
– |
endTest = &(simnfo->finalName[nameLength - 4]); |
567 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
568 |
– |
strcpy( endTest, ".eor" ); |
569 |
– |
} |
570 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
571 |
– |
strcpy( endTest, ".eor" ); |
572 |
– |
} |
573 |
– |
else{ |
574 |
– |
strcat( simnfo->finalName, ".eor" ); |
575 |
– |
} |
576 |
– |
} |
577 |
– |
} |
578 |
– |
|
579 |
– |
// make the sample and status out names |
580 |
– |
|
581 |
– |
strcpy( simnfo->sampleName, inFileName ); |
582 |
– |
char* endTest; |
583 |
– |
int nameLength = strlen( simnfo->sampleName ); |
584 |
– |
endTest = &(simnfo->sampleName[nameLength - 5]); |
585 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
586 |
– |
strcpy( endTest, ".dump" ); |
587 |
– |
} |
588 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
589 |
– |
strcpy( endTest, ".dump" ); |
590 |
– |
} |
591 |
– |
else{ |
592 |
– |
endTest = &(simnfo->sampleName[nameLength - 4]); |
593 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
594 |
– |
strcpy( endTest, ".dump" ); |
595 |
– |
} |
596 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
597 |
– |
strcpy( endTest, ".dump" ); |
598 |
– |
} |
599 |
– |
else{ |
600 |
– |
strcat( simnfo->sampleName, ".dump" ); |
601 |
– |
} |
602 |
– |
} |
603 |
– |
|
604 |
– |
strcpy( simnfo->statusName, inFileName ); |
605 |
– |
nameLength = strlen( simnfo->statusName ); |
606 |
– |
endTest = &(simnfo->statusName[nameLength - 5]); |
607 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
608 |
– |
strcpy( endTest, ".stat" ); |
609 |
– |
} |
610 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
611 |
– |
strcpy( endTest, ".stat" ); |
612 |
– |
} |
613 |
– |
else{ |
614 |
– |
endTest = &(simnfo->statusName[nameLength - 4]); |
615 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
616 |
– |
strcpy( endTest, ".stat" ); |
617 |
– |
} |
618 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
619 |
– |
strcpy( endTest, ".stat" ); |
620 |
– |
} |
621 |
– |
else{ |
622 |
– |
strcat( simnfo->statusName, ".stat" ); |
623 |
– |
} |
624 |
– |
} |
625 |
– |
|
626 |
– |
#ifdef IS_MPI |
627 |
– |
} |
628 |
– |
#endif // is_mpi |
629 |
– |
|
630 |
– |
// set the status, sample, and themal kick times |
631 |
– |
|
632 |
– |
if( the_globals->haveSampleTime() ){ |
633 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
634 |
– |
simnfo->statusTime = simnfo->sampleTime; |
635 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
636 |
– |
} |
637 |
– |
else{ |
638 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
639 |
– |
simnfo->statusTime = simnfo->sampleTime; |
640 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
641 |
– |
} |
642 |
– |
|
643 |
– |
if( the_globals->haveStatusTime() ){ |
644 |
– |
simnfo->statusTime = the_globals->getStatusTime(); |
645 |
– |
} |
646 |
– |
|
647 |
– |
if( the_globals->haveThermalTime() ){ |
648 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
649 |
– |
} |
650 |
– |
|
651 |
– |
// check for the temperature set flag |
652 |
– |
|
653 |
– |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
654 |
– |
|
655 |
– |
|
656 |
– |
// // make the longe range forces and the integrator |
657 |
– |
|
658 |
– |
// new AllLong( simnfo ); |
659 |
– |
|
660 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
661 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
662 |
– |
|
663 |
– |
|
664 |
– |
|
665 |
– |
// initialize the Fortran |
666 |
– |
|
667 |
– |
simnfo->refreshSim(); |
668 |
– |
|
669 |
– |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
670 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
671 |
– |
} |
672 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
673 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
674 |
– |
} |
675 |
– |
else{ |
676 |
– |
sprintf( painCave.errMsg, |
677 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
678 |
– |
simnfo->mixingRule ); |
679 |
– |
painCave.isFatal = 1; |
680 |
– |
simError(); |
681 |
– |
} |
682 |
– |
|
683 |
– |
|
684 |
– |
#ifdef IS_MPI |
685 |
– |
strcpy( checkPointMsg, |
686 |
– |
"Successfully intialized the mixingRule for Fortran." ); |
687 |
– |
MPIcheckPoint(); |
688 |
– |
#endif // is_mpi |
118 |
|
} |
119 |
|
|
120 |
|
|
121 |
|
void SimSetup::makeMolecules( void ){ |
122 |
|
|
123 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
124 |
< |
molInit info; |
124 |
> |
molInit molInfo; |
125 |
|
DirectionalAtom* dAtom; |
126 |
|
LinkedAssign* extras; |
127 |
|
LinkedAssign* current_extra; |
146 |
|
|
147 |
|
atomOffset = 0; |
148 |
|
excludeOffset = 0; |
149 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
149 |
> |
for(i=0; i<info->n_mol; i++){ |
150 |
|
|
151 |
|
stampID = the_molecules[i].getStampID(); |
152 |
|
|
153 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
156 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
153 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
158 |
|
|
159 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
160 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
161 |
< |
info.myBonds = new Bond*[info.nBonds]; |
162 |
< |
info.myBends = new Bend*[info.nBends]; |
163 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
159 |
> |
molInfo.myAtoms = &the_atoms[atomOffset]; |
160 |
> |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
161 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
162 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
163 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
164 |
|
|
165 |
< |
theBonds = new bond_pair[info.nBonds]; |
166 |
< |
theBends = new bend_set[info.nBends]; |
167 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
165 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
166 |
> |
theBends = new bend_set[molInfo.nBends]; |
167 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
168 |
|
|
169 |
|
// make the Atoms |
170 |
|
|
171 |
< |
for(j=0; j<info.nAtoms; j++){ |
171 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
172 |
|
|
173 |
|
currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 |
|
if( currentAtom->haveOrientation() ){ |
175 |
|
|
176 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
177 |
< |
simnfo->n_oriented++; |
178 |
< |
info.myAtoms[j] = dAtom; |
177 |
> |
info->n_oriented++; |
178 |
> |
molInfo.myAtoms[j] = dAtom; |
179 |
|
|
180 |
|
ux = currentAtom->getOrntX(); |
181 |
|
uy = currentAtom->getOrntY(); |
193 |
|
dAtom->setSUz( uz ); |
194 |
|
} |
195 |
|
else{ |
196 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
196 |
> |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 |
|
} |
198 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
198 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
199 |
|
|
200 |
|
#ifdef IS_MPI |
201 |
|
|
202 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
202 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 |
|
|
204 |
|
#endif // is_mpi |
205 |
|
} |
206 |
|
|
207 |
|
// make the bonds |
208 |
< |
for(j=0; j<info.nBonds; j++){ |
208 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
209 |
|
|
210 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
211 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
212 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
213 |
|
|
214 |
< |
exI = theBonds[i].a; |
215 |
< |
exJ = theBonds[i].b; |
214 |
> |
exI = theBonds[j].a; |
215 |
> |
exJ = theBonds[j].b; |
216 |
|
|
217 |
|
// exclude_I must always be the smaller of the pair |
218 |
|
if( exI > exJ ){ |
228 |
|
|
229 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
230 |
|
#else // isn't MPI |
231 |
+ |
|
232 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
233 |
|
#endif //is_mpi |
234 |
|
} |
235 |
< |
excludeOffset += info.nBonds; |
235 |
> |
excludeOffset += molInfo.nBonds; |
236 |
|
|
237 |
|
//make the bends |
238 |
< |
for(j=0; j<info.nBends; j++){ |
238 |
> |
for(j=0; j<molInfo.nBends; j++){ |
239 |
|
|
240 |
|
currentBend = comp_stamps[stampID]->getBend( j ); |
241 |
|
theBends[j].a = currentBend->getA() + atomOffset; |
266 |
|
|
267 |
|
default: |
268 |
|
sprintf( painCave.errMsg, |
269 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
269 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
270 |
|
"double nor an int.\n" |
271 |
|
"-->Bend[%d] in %s\n", |
272 |
|
j, comp_stamps[stampID]->getID() ); |
318 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 |
|
#endif //is_mpi |
320 |
|
} |
321 |
< |
excludeOffset += info.nBends; |
321 |
> |
excludeOffset += molInfo.nBends; |
322 |
|
|
323 |
< |
for(j=0; j<info.nTorsions; j++){ |
323 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
324 |
|
|
325 |
|
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 |
|
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
348 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
|
#endif //is_mpi |
350 |
|
} |
351 |
< |
excludeOffset += info.nTorsions; |
351 |
> |
excludeOffset += molInfo.nTorsions; |
352 |
|
|
353 |
|
|
354 |
|
// send the arrays off to the forceField for init. |
355 |
|
|
356 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
357 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
358 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
359 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
356 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 |
|
|
361 |
|
|
362 |
< |
the_molecules[i].initialize( info ); |
363 |
< |
atomOffset += info.nAtoms; |
362 |
> |
the_molecules[i].initialize( molInfo ); |
363 |
> |
|
364 |
> |
|
365 |
> |
atomOffset += molInfo.nAtoms; |
366 |
|
delete[] theBonds; |
367 |
|
delete[] theBends; |
368 |
|
delete[] theTorsions; |
369 |
|
} |
370 |
|
|
371 |
+ |
#ifdef IS_MPI |
372 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
373 |
+ |
MPIcheckPoint(); |
374 |
+ |
#endif // is_mpi |
375 |
+ |
|
376 |
|
// clean up the forcefield |
377 |
|
the_ff->calcRcut(); |
378 |
|
the_ff->cleanMe(); |
379 |
+ |
|
380 |
|
} |
381 |
|
|
382 |
|
void SimSetup::initFromBass( void ){ |
398 |
|
have_extra =1; |
399 |
|
|
400 |
|
n_cells = (int)temp3 - 1; |
401 |
< |
cellx = simnfo->box_x / temp3; |
402 |
< |
celly = simnfo->box_y / temp3; |
403 |
< |
cellz = simnfo->box_z / temp3; |
401 |
> |
cellx = info->boxL[0] / temp3; |
402 |
> |
celly = info->boxL[1] / temp3; |
403 |
> |
cellz = info->boxL[2] / temp3; |
404 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 |
|
n_per_extra = (int)ceil( temp1 ); |
415 |
|
} |
416 |
|
else{ |
417 |
|
n_cells = (int)temp3; |
418 |
< |
cellx = simnfo->box_x / temp3; |
419 |
< |
celly = simnfo->box_y / temp3; |
420 |
< |
cellz = simnfo->box_z / temp3; |
418 |
> |
cellx = info->boxL[0] / temp3; |
419 |
> |
celly = info->boxL[1] / temp3; |
420 |
> |
cellz = info->boxL[2] / temp3; |
421 |
|
} |
422 |
|
|
423 |
|
current_mol = 0; |
497 |
|
} |
498 |
|
|
499 |
|
|
500 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
501 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
502 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
503 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
500 |
> |
for( i=0; i<info->n_atoms; i++ ){ |
501 |
> |
info->atoms[i]->set_vx( 0.0 ); |
502 |
> |
info->atoms[i]->set_vy( 0.0 ); |
503 |
> |
info->atoms[i]->set_vz( 0.0 ); |
504 |
|
} |
505 |
|
} |
506 |
|
|
559 |
|
|
560 |
|
current_comp_mol = 0; |
561 |
|
current_comp++; |
562 |
+ |
} |
563 |
+ |
} |
564 |
+ |
|
565 |
+ |
|
566 |
+ |
void SimSetup::gatherInfo( void ){ |
567 |
+ |
int i,j,k; |
568 |
+ |
|
569 |
+ |
ensembleCase = -1; |
570 |
+ |
ffCase = -1; |
571 |
+ |
|
572 |
+ |
// get the stamps and globals; |
573 |
+ |
stamps = stamps; |
574 |
+ |
globals = globals; |
575 |
+ |
|
576 |
+ |
// set the easy ones first |
577 |
+ |
info->target_temp = globals->getTargetTemp(); |
578 |
+ |
info->dt = globals->getDt(); |
579 |
+ |
info->run_time = globals->getRunTime(); |
580 |
+ |
n_components = globals->getNComponents(); |
581 |
+ |
|
582 |
+ |
|
583 |
+ |
// get the forceField |
584 |
+ |
|
585 |
+ |
strcpy( force_field, globals->getForceField() ); |
586 |
+ |
|
587 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
588 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
589 |
+ |
else{ |
590 |
+ |
sprintf( painCave.errMsg, |
591 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
592 |
+ |
force_field ); |
593 |
+ |
painCave.isFatal = 1; |
594 |
+ |
simError(); |
595 |
+ |
} |
596 |
+ |
|
597 |
+ |
// get the ensemble |
598 |
+ |
|
599 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
600 |
+ |
|
601 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
602 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
603 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
604 |
+ |
ensembleCase = NPTi_ENS; |
605 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
606 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
607 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
608 |
+ |
else{ |
609 |
+ |
sprintf( painCave.errMsg, |
610 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
611 |
+ |
"reverting to NVE for this simulation.\n", |
612 |
+ |
ensemble ); |
613 |
+ |
painCave.isFatal = 0; |
614 |
+ |
simError(); |
615 |
+ |
strcpy( ensemble, "NVE" ); |
616 |
+ |
ensembleCase = NVE_ENS; |
617 |
+ |
} |
618 |
+ |
strcpy( info->ensemble, ensemble ); |
619 |
+ |
|
620 |
+ |
// get the mixing rule |
621 |
+ |
|
622 |
+ |
strcpy( info->mixingRule, globals->getMixingRule() ); |
623 |
+ |
info->usePBC = globals->getPBC(); |
624 |
+ |
|
625 |
+ |
|
626 |
+ |
// get the components and calculate the tot_nMol and indvidual n_mol |
627 |
+ |
|
628 |
+ |
the_components = globals->getComponents(); |
629 |
+ |
components_nmol = new int[n_components]; |
630 |
+ |
|
631 |
+ |
|
632 |
+ |
if( !globals->haveNMol() ){ |
633 |
+ |
// we don't have the total number of molecules, so we assume it is |
634 |
+ |
// given in each component |
635 |
+ |
|
636 |
+ |
tot_nmol = 0; |
637 |
+ |
for( i=0; i<n_components; i++ ){ |
638 |
+ |
|
639 |
+ |
if( !the_components[i]->haveNMol() ){ |
640 |
+ |
// we have a problem |
641 |
+ |
sprintf( painCave.errMsg, |
642 |
+ |
"SimSetup Error. No global NMol or component NMol" |
643 |
+ |
" given. Cannot calculate the number of atoms.\n" ); |
644 |
+ |
painCave.isFatal = 1; |
645 |
+ |
simError(); |
646 |
+ |
} |
647 |
+ |
|
648 |
+ |
tot_nmol += the_components[i]->getNMol(); |
649 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
650 |
+ |
} |
651 |
+ |
} |
652 |
+ |
else{ |
653 |
+ |
sprintf( painCave.errMsg, |
654 |
+ |
"SimSetup error.\n" |
655 |
+ |
"\tSorry, the ability to specify total" |
656 |
+ |
" nMols and then give molfractions in the components\n" |
657 |
+ |
"\tis not currently supported." |
658 |
+ |
" Please give nMol in the components.\n" ); |
659 |
+ |
painCave.isFatal = 1; |
660 |
+ |
simError(); |
661 |
|
} |
662 |
+ |
|
663 |
+ |
// set the status, sample, and thermal kick times |
664 |
+ |
|
665 |
+ |
if( globals->haveSampleTime() ){ |
666 |
+ |
info->sampleTime = globals->getSampleTime(); |
667 |
+ |
info->statusTime = info->sampleTime; |
668 |
+ |
info->thermalTime = info->sampleTime; |
669 |
+ |
} |
670 |
+ |
else{ |
671 |
+ |
info->sampleTime = globals->getRunTime(); |
672 |
+ |
info->statusTime = info->sampleTime; |
673 |
+ |
info->thermalTime = info->sampleTime; |
674 |
+ |
} |
675 |
+ |
|
676 |
+ |
if( globals->haveStatusTime() ){ |
677 |
+ |
info->statusTime = globals->getStatusTime(); |
678 |
+ |
} |
679 |
+ |
|
680 |
+ |
if( globals->haveThermalTime() ){ |
681 |
+ |
info->thermalTime = globals->getThermalTime(); |
682 |
+ |
} |
683 |
+ |
|
684 |
+ |
// check for the temperature set flag |
685 |
+ |
|
686 |
+ |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 |
+ |
|
688 |
+ |
// get some of the tricky things that may still be in the globals |
689 |
+ |
|
690 |
+ |
double boxVector[3]; |
691 |
+ |
if( globals->haveBox() ){ |
692 |
+ |
boxVector[0] = globals->getBox(); |
693 |
+ |
boxVector[1] = globals->getBox(); |
694 |
+ |
boxVector[2] = globals->getBox(); |
695 |
+ |
|
696 |
+ |
info->setBox( boxVector ); |
697 |
+ |
} |
698 |
+ |
else if( globals->haveDensity() ){ |
699 |
+ |
|
700 |
+ |
double vol; |
701 |
+ |
vol = (double)tot_nmol / globals->getDensity(); |
702 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
+ |
boxVector[1] = boxVector[0]; |
704 |
+ |
boxVector[2] = boxVector[0]; |
705 |
+ |
|
706 |
+ |
info->setBox( boxVector ); |
707 |
+ |
} |
708 |
+ |
else{ |
709 |
+ |
if( !globals->haveBoxX() ){ |
710 |
+ |
sprintf( painCave.errMsg, |
711 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
+ |
painCave.isFatal = 1; |
713 |
+ |
simError(); |
714 |
+ |
} |
715 |
+ |
boxVector[0] = globals->getBoxX(); |
716 |
+ |
|
717 |
+ |
if( !globals->haveBoxY() ){ |
718 |
+ |
sprintf( painCave.errMsg, |
719 |
+ |
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
+ |
painCave.isFatal = 1; |
721 |
+ |
simError(); |
722 |
+ |
} |
723 |
+ |
boxVector[1] = globals->getBoxY(); |
724 |
+ |
|
725 |
+ |
if( !globals->haveBoxZ() ){ |
726 |
+ |
sprintf( painCave.errMsg, |
727 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
728 |
+ |
painCave.isFatal = 1; |
729 |
+ |
simError(); |
730 |
+ |
} |
731 |
+ |
boxVector[2] = globals->getBoxZ(); |
732 |
+ |
|
733 |
+ |
info->setBox( boxVector ); |
734 |
+ |
} |
735 |
+ |
|
736 |
+ |
|
737 |
+ |
|
738 |
+ |
#ifdef IS_MPI |
739 |
+ |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
740 |
+ |
MPIcheckPoint(); |
741 |
+ |
#endif // is_mpi |
742 |
+ |
|
743 |
|
} |
744 |
+ |
|
745 |
+ |
|
746 |
+ |
void SimSetup::finalInfoCheck( void ){ |
747 |
+ |
int index; |
748 |
+ |
int usesDipoles; |
749 |
+ |
|
750 |
+ |
|
751 |
+ |
// check electrostatic parameters |
752 |
+ |
|
753 |
+ |
index = 0; |
754 |
+ |
usesDipoles = 0; |
755 |
+ |
while( (index < info->n_atoms) && !usesDipoles ){ |
756 |
+ |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
757 |
+ |
index++; |
758 |
+ |
} |
759 |
+ |
|
760 |
+ |
#ifdef IS_MPI |
761 |
+ |
int myUse = usesDipoles; |
762 |
+ |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
763 |
+ |
#endif //is_mpi |
764 |
+ |
|
765 |
+ |
|
766 |
+ |
if (globals->getUseRF() ) { |
767 |
+ |
info->useReactionField = 1; |
768 |
+ |
|
769 |
+ |
if( !globals->haveECR() ){ |
770 |
+ |
sprintf( painCave.errMsg, |
771 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
772 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
773 |
+ |
"I hope you have a very fast processor!\n"); |
774 |
+ |
painCave.isFatal = 0; |
775 |
+ |
simError(); |
776 |
+ |
double smallest; |
777 |
+ |
smallest = info->boxL[0]; |
778 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
779 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
780 |
+ |
info->ecr = 0.5 * smallest; |
781 |
+ |
} else { |
782 |
+ |
info->ecr = globals->getECR(); |
783 |
+ |
} |
784 |
+ |
|
785 |
+ |
if( !globals->haveEST() ){ |
786 |
+ |
sprintf( painCave.errMsg, |
787 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
788 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
789 |
+ |
); |
790 |
+ |
painCave.isFatal = 0; |
791 |
+ |
simError(); |
792 |
+ |
info->est = 0.05 * info->ecr; |
793 |
+ |
} else { |
794 |
+ |
info->est = globals->getEST(); |
795 |
+ |
} |
796 |
+ |
|
797 |
+ |
if(!globals->haveDielectric() ){ |
798 |
+ |
sprintf( painCave.errMsg, |
799 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
800 |
+ |
"setting a dielectric constant!\n" |
801 |
+ |
); |
802 |
+ |
painCave.isFatal = 1; |
803 |
+ |
simError(); |
804 |
+ |
} |
805 |
+ |
info->dielectric = globals->getDielectric(); |
806 |
+ |
} |
807 |
+ |
else { |
808 |
+ |
if (usesDipoles) { |
809 |
+ |
|
810 |
+ |
if( !globals->haveECR() ){ |
811 |
+ |
sprintf( painCave.errMsg, |
812 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
813 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
814 |
+ |
"I hope you have a very fast processor!\n"); |
815 |
+ |
painCave.isFatal = 0; |
816 |
+ |
simError(); |
817 |
+ |
double smallest; |
818 |
+ |
smallest = info->boxL[0]; |
819 |
+ |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
820 |
+ |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
821 |
+ |
info->ecr = 0.5 * smallest; |
822 |
+ |
} else { |
823 |
+ |
info->ecr = globals->getECR(); |
824 |
+ |
} |
825 |
+ |
|
826 |
+ |
if( !globals->haveEST() ){ |
827 |
+ |
sprintf( painCave.errMsg, |
828 |
+ |
"SimSetup Warning: using default value of 5%% of the " |
829 |
+ |
"electrostaticCutoffRadius for the " |
830 |
+ |
"electrostaticSkinThickness\n" |
831 |
+ |
); |
832 |
+ |
painCave.isFatal = 0; |
833 |
+ |
simError(); |
834 |
+ |
info->est = 0.05 * info->ecr; |
835 |
+ |
} else { |
836 |
+ |
info->est = globals->getEST(); |
837 |
+ |
} |
838 |
+ |
} |
839 |
+ |
} |
840 |
+ |
|
841 |
+ |
#ifdef IS_MPI |
842 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
843 |
+ |
MPIcheckPoint(); |
844 |
+ |
#endif // is_mpi |
845 |
+ |
|
846 |
+ |
} |
847 |
+ |
|
848 |
+ |
void SimSetup::initSystemCoords( void ){ |
849 |
+ |
|
850 |
+ |
if( globals->haveInitialConfig() ){ |
851 |
+ |
|
852 |
+ |
InitializeFromFile* fileInit; |
853 |
+ |
#ifdef IS_MPI // is_mpi |
854 |
+ |
if( worldRank == 0 ){ |
855 |
+ |
#endif //is_mpi |
856 |
+ |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
857 |
+ |
#ifdef IS_MPI |
858 |
+ |
}else fileInit = new InitializeFromFile( NULL ); |
859 |
+ |
#endif |
860 |
+ |
fileInit->read_xyz( info ); // default velocities on |
861 |
+ |
|
862 |
+ |
delete fileInit; |
863 |
+ |
} |
864 |
+ |
else{ |
865 |
+ |
|
866 |
+ |
#ifdef IS_MPI |
867 |
+ |
|
868 |
+ |
// no init from bass |
869 |
+ |
|
870 |
+ |
sprintf( painCave.errMsg, |
871 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
872 |
+ |
painCave.isFatal; |
873 |
+ |
simError(); |
874 |
+ |
|
875 |
+ |
#else |
876 |
+ |
|
877 |
+ |
initFromBass(); |
878 |
+ |
|
879 |
+ |
|
880 |
+ |
#endif |
881 |
+ |
} |
882 |
+ |
|
883 |
+ |
#ifdef IS_MPI |
884 |
+ |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
885 |
+ |
MPIcheckPoint(); |
886 |
+ |
#endif // is_mpi |
887 |
+ |
|
888 |
+ |
} |
889 |
+ |
|
890 |
+ |
|
891 |
+ |
void SimSetup::makeOutNames( void ){ |
892 |
+ |
|
893 |
+ |
#ifdef IS_MPI |
894 |
+ |
if( worldRank == 0 ){ |
895 |
+ |
#endif // is_mpi |
896 |
+ |
|
897 |
+ |
if( globals->haveFinalConfig() ){ |
898 |
+ |
strcpy( info->finalName, globals->getFinalConfig() ); |
899 |
+ |
} |
900 |
+ |
else{ |
901 |
+ |
strcpy( info->finalName, inFileName ); |
902 |
+ |
char* endTest; |
903 |
+ |
int nameLength = strlen( info->finalName ); |
904 |
+ |
endTest = &(info->finalName[nameLength - 5]); |
905 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
906 |
+ |
strcpy( endTest, ".eor" ); |
907 |
+ |
} |
908 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
909 |
+ |
strcpy( endTest, ".eor" ); |
910 |
+ |
} |
911 |
+ |
else{ |
912 |
+ |
endTest = &(info->finalName[nameLength - 4]); |
913 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
914 |
+ |
strcpy( endTest, ".eor" ); |
915 |
+ |
} |
916 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
917 |
+ |
strcpy( endTest, ".eor" ); |
918 |
+ |
} |
919 |
+ |
else{ |
920 |
+ |
strcat( info->finalName, ".eor" ); |
921 |
+ |
} |
922 |
+ |
} |
923 |
+ |
} |
924 |
+ |
|
925 |
+ |
// make the sample and status out names |
926 |
+ |
|
927 |
+ |
strcpy( info->sampleName, inFileName ); |
928 |
+ |
char* endTest; |
929 |
+ |
int nameLength = strlen( info->sampleName ); |
930 |
+ |
endTest = &(info->sampleName[nameLength - 5]); |
931 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
932 |
+ |
strcpy( endTest, ".dump" ); |
933 |
+ |
} |
934 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
935 |
+ |
strcpy( endTest, ".dump" ); |
936 |
+ |
} |
937 |
+ |
else{ |
938 |
+ |
endTest = &(info->sampleName[nameLength - 4]); |
939 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
940 |
+ |
strcpy( endTest, ".dump" ); |
941 |
+ |
} |
942 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
943 |
+ |
strcpy( endTest, ".dump" ); |
944 |
+ |
} |
945 |
+ |
else{ |
946 |
+ |
strcat( info->sampleName, ".dump" ); |
947 |
+ |
} |
948 |
+ |
} |
949 |
+ |
|
950 |
+ |
strcpy( info->statusName, inFileName ); |
951 |
+ |
nameLength = strlen( info->statusName ); |
952 |
+ |
endTest = &(info->statusName[nameLength - 5]); |
953 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
954 |
+ |
strcpy( endTest, ".stat" ); |
955 |
+ |
} |
956 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
957 |
+ |
strcpy( endTest, ".stat" ); |
958 |
+ |
} |
959 |
+ |
else{ |
960 |
+ |
endTest = &(info->statusName[nameLength - 4]); |
961 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
962 |
+ |
strcpy( endTest, ".stat" ); |
963 |
+ |
} |
964 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
965 |
+ |
strcpy( endTest, ".stat" ); |
966 |
+ |
} |
967 |
+ |
else{ |
968 |
+ |
strcat( info->statusName, ".stat" ); |
969 |
+ |
} |
970 |
+ |
} |
971 |
+ |
|
972 |
+ |
#ifdef IS_MPI |
973 |
+ |
} |
974 |
+ |
#endif // is_mpi |
975 |
+ |
|
976 |
+ |
} |
977 |
+ |
|
978 |
+ |
|
979 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
980 |
+ |
|
981 |
+ |
int i; |
982 |
+ |
|
983 |
+ |
// create the forceField |
984 |
+ |
|
985 |
+ |
createFF(); |
986 |
+ |
|
987 |
+ |
// extract componentList |
988 |
+ |
|
989 |
+ |
compList(); |
990 |
+ |
|
991 |
+ |
// calc the number of atoms, bond, bends, and torsions |
992 |
+ |
|
993 |
+ |
calcSysValues(); |
994 |
+ |
|
995 |
+ |
#ifdef IS_MPI |
996 |
+ |
// divide the molecules among the processors |
997 |
+ |
|
998 |
+ |
mpiMolDivide(); |
999 |
+ |
#endif //is_mpi |
1000 |
+ |
|
1001 |
+ |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1002 |
+ |
|
1003 |
+ |
makeSysArrays(); |
1004 |
+ |
|
1005 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1006 |
+ |
|
1007 |
+ |
makeMolecules(); |
1008 |
+ |
info->identArray = new int[info->n_atoms]; |
1009 |
+ |
for(i=0; i<info->n_atoms; i++){ |
1010 |
+ |
info->identArray[i] = the_atoms[i]->getIdent(); |
1011 |
+ |
} |
1012 |
+ |
|
1013 |
+ |
|
1014 |
+ |
|
1015 |
+ |
} |
1016 |
+ |
|
1017 |
+ |
|
1018 |
+ |
void SimSetup::createFF( void ){ |
1019 |
+ |
|
1020 |
+ |
switch( ffCase ){ |
1021 |
+ |
|
1022 |
+ |
case FF_DUFF: |
1023 |
+ |
the_ff = new DUFF(); |
1024 |
+ |
break; |
1025 |
+ |
|
1026 |
+ |
case FF_LJ: |
1027 |
+ |
the_ff = new LJFF(); |
1028 |
+ |
break; |
1029 |
+ |
|
1030 |
+ |
default: |
1031 |
+ |
sprintf( painCave.errMsg, |
1032 |
+ |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1033 |
+ |
painCave.isFatal = 1; |
1034 |
+ |
simError(); |
1035 |
+ |
} |
1036 |
+ |
|
1037 |
+ |
#ifdef IS_MPI |
1038 |
+ |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1039 |
+ |
MPIcheckPoint(); |
1040 |
+ |
#endif // is_mpi |
1041 |
+ |
|
1042 |
+ |
} |
1043 |
+ |
|
1044 |
+ |
|
1045 |
+ |
void SimSetup::compList( void ){ |
1046 |
+ |
|
1047 |
+ |
int i; |
1048 |
+ |
|
1049 |
+ |
comp_stamps = new MoleculeStamp*[n_components]; |
1050 |
+ |
|
1051 |
+ |
// make an array of molecule stamps that match the components used. |
1052 |
+ |
// also extract the used stamps out into a separate linked list |
1053 |
+ |
|
1054 |
+ |
info->nComponents = n_components; |
1055 |
+ |
info->componentsNmol = components_nmol; |
1056 |
+ |
info->compStamps = comp_stamps; |
1057 |
+ |
info->headStamp = new LinkedMolStamp(); |
1058 |
+ |
|
1059 |
+ |
char* id; |
1060 |
+ |
LinkedMolStamp* headStamp = info->headStamp; |
1061 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1062 |
+ |
for( i=0; i<n_components; i++ ){ |
1063 |
+ |
|
1064 |
+ |
id = the_components[i]->getType(); |
1065 |
+ |
comp_stamps[i] = NULL; |
1066 |
+ |
|
1067 |
+ |
// check to make sure the component isn't already in the list |
1068 |
+ |
|
1069 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1070 |
+ |
if( comp_stamps[i] == NULL ){ |
1071 |
+ |
|
1072 |
+ |
// extract the component from the list; |
1073 |
+ |
|
1074 |
+ |
currentStamp = stamps->extractMolStamp( id ); |
1075 |
+ |
if( currentStamp == NULL ){ |
1076 |
+ |
sprintf( painCave.errMsg, |
1077 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1078 |
+ |
"list of declared molecules\n", |
1079 |
+ |
id ); |
1080 |
+ |
painCave.isFatal = 1; |
1081 |
+ |
simError(); |
1082 |
+ |
} |
1083 |
+ |
|
1084 |
+ |
headStamp->add( currentStamp ); |
1085 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1086 |
+ |
} |
1087 |
+ |
} |
1088 |
+ |
|
1089 |
+ |
#ifdef IS_MPI |
1090 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1091 |
+ |
MPIcheckPoint(); |
1092 |
+ |
#endif // is_mpi |
1093 |
+ |
|
1094 |
+ |
|
1095 |
+ |
} |
1096 |
+ |
|
1097 |
+ |
void SimSetup::calcSysValues( void ){ |
1098 |
+ |
int i, j, k; |
1099 |
+ |
|
1100 |
+ |
|
1101 |
+ |
tot_atoms = 0; |
1102 |
+ |
tot_bonds = 0; |
1103 |
+ |
tot_bends = 0; |
1104 |
+ |
tot_torsions = 0; |
1105 |
+ |
for( i=0; i<n_components; i++ ){ |
1106 |
+ |
|
1107 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1108 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1109 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1110 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1111 |
+ |
} |
1112 |
+ |
|
1113 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1114 |
+ |
|
1115 |
+ |
info->n_atoms = tot_atoms; |
1116 |
+ |
info->n_bonds = tot_bonds; |
1117 |
+ |
info->n_bends = tot_bends; |
1118 |
+ |
info->n_torsions = tot_torsions; |
1119 |
+ |
info->n_SRI = tot_SRI; |
1120 |
+ |
info->n_mol = tot_nmol; |
1121 |
+ |
|
1122 |
+ |
info->molMembershipArray = new int[tot_atoms]; |
1123 |
+ |
} |
1124 |
+ |
|
1125 |
+ |
|
1126 |
+ |
#ifdef IS_MPI |
1127 |
+ |
|
1128 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1129 |
+ |
|
1130 |
+ |
int i, j, k; |
1131 |
+ |
int localMol, allMol; |
1132 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1133 |
+ |
|
1134 |
+ |
mpiSim = new mpiSimulation( info ); |
1135 |
+ |
|
1136 |
+ |
globalIndex = mpiSim->divideLabor(); |
1137 |
+ |
|
1138 |
+ |
// set up the local variables |
1139 |
+ |
|
1140 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1141 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1142 |
+ |
|
1143 |
+ |
allMol = 0; |
1144 |
+ |
localMol = 0; |
1145 |
+ |
local_atoms = 0; |
1146 |
+ |
local_bonds = 0; |
1147 |
+ |
local_bends = 0; |
1148 |
+ |
local_torsions = 0; |
1149 |
+ |
globalAtomIndex = 0; |
1150 |
+ |
|
1151 |
+ |
|
1152 |
+ |
for( i=0; i<n_components; i++ ){ |
1153 |
+ |
|
1154 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1155 |
+ |
|
1156 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1157 |
+ |
|
1158 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1159 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1160 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1161 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1162 |
+ |
localMol++; |
1163 |
+ |
} |
1164 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1165 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1166 |
+ |
globalAtomIndex++; |
1167 |
+ |
} |
1168 |
+ |
|
1169 |
+ |
allMol++; |
1170 |
+ |
} |
1171 |
+ |
} |
1172 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1173 |
+ |
|
1174 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1175 |
+ |
|
1176 |
+ |
if( local_atoms != info->n_atoms ){ |
1177 |
+ |
sprintf( painCave.errMsg, |
1178 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1179 |
+ |
" localAtom (%d) are not equal.\n", |
1180 |
+ |
info->n_atoms, |
1181 |
+ |
local_atoms ); |
1182 |
+ |
painCave.isFatal = 1; |
1183 |
+ |
simError(); |
1184 |
+ |
} |
1185 |
+ |
|
1186 |
+ |
info->n_bonds = local_bonds; |
1187 |
+ |
info->n_bends = local_bends; |
1188 |
+ |
info->n_torsions = local_torsions; |
1189 |
+ |
info->n_SRI = local_SRI; |
1190 |
+ |
info->n_mol = localMol; |
1191 |
+ |
|
1192 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1193 |
+ |
MPIcheckPoint(); |
1194 |
+ |
} |
1195 |
+ |
|
1196 |
+ |
#endif // is_mpi |
1197 |
+ |
|
1198 |
+ |
|
1199 |
+ |
void SimSetup::makeSysArrays( void ){ |
1200 |
+ |
int i, j, k; |
1201 |
+ |
|
1202 |
+ |
|
1203 |
+ |
// create the atom and short range interaction arrays |
1204 |
+ |
|
1205 |
+ |
Atom::createArrays(info->n_atoms); |
1206 |
+ |
the_atoms = new Atom*[info->n_atoms]; |
1207 |
+ |
the_molecules = new Molecule[info->n_mol]; |
1208 |
+ |
int molIndex; |
1209 |
+ |
|
1210 |
+ |
// initialize the molecule's stampID's |
1211 |
+ |
|
1212 |
+ |
#ifdef IS_MPI |
1213 |
+ |
|
1214 |
+ |
|
1215 |
+ |
molIndex = 0; |
1216 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1217 |
+ |
|
1218 |
+ |
if(mol2proc[i] == worldRank ){ |
1219 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1220 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1221 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1222 |
+ |
molIndex++; |
1223 |
+ |
} |
1224 |
+ |
} |
1225 |
+ |
|
1226 |
+ |
#else // is_mpi |
1227 |
+ |
|
1228 |
+ |
molIndex = 0; |
1229 |
+ |
globalAtomIndex = 0; |
1230 |
+ |
for(i=0; i<n_components; i++){ |
1231 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1232 |
+ |
the_molecules[molIndex].setStampID( i ); |
1233 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1234 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1235 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1236 |
+ |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1237 |
+ |
globalAtomIndex++; |
1238 |
+ |
} |
1239 |
+ |
molIndex++; |
1240 |
+ |
} |
1241 |
+ |
} |
1242 |
+ |
|
1243 |
+ |
|
1244 |
+ |
#endif // is_mpi |
1245 |
+ |
|
1246 |
+ |
|
1247 |
+ |
if( info->n_SRI ){ |
1248 |
+ |
|
1249 |
+ |
Exclude::createArray(info->n_SRI); |
1250 |
+ |
the_excludes = new Exclude*[info->n_SRI]; |
1251 |
+ |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1252 |
+ |
info->globalExcludes = new int; |
1253 |
+ |
info->n_exclude = info->n_SRI; |
1254 |
+ |
} |
1255 |
+ |
else{ |
1256 |
+ |
|
1257 |
+ |
Exclude::createArray( 1 ); |
1258 |
+ |
the_excludes = new Exclude*; |
1259 |
+ |
the_excludes[0] = new Exclude(0); |
1260 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1261 |
+ |
info->globalExcludes = new int; |
1262 |
+ |
info->globalExcludes[0] = 0; |
1263 |
+ |
info->n_exclude = 0; |
1264 |
+ |
} |
1265 |
+ |
|
1266 |
+ |
// set the arrays into the SimInfo object |
1267 |
+ |
|
1268 |
+ |
info->atoms = the_atoms; |
1269 |
+ |
info->molecules = the_molecules; |
1270 |
+ |
info->nGlobalExcludes = 0; |
1271 |
+ |
info->excludes = the_excludes; |
1272 |
+ |
|
1273 |
+ |
the_ff->setSimInfo( info ); |
1274 |
+ |
|
1275 |
+ |
} |
1276 |
+ |
|
1277 |
+ |
void SimSetup::makeIntegrator( void ){ |
1278 |
+ |
|
1279 |
+ |
NVT* myNVT = NULL; |
1280 |
+ |
NPTi* myNPTi = NULL; |
1281 |
+ |
NPTf* myNPTf = NULL; |
1282 |
+ |
NPTim* myNPTim = NULL; |
1283 |
+ |
NPTfm* myNPTfm = NULL; |
1284 |
+ |
|
1285 |
+ |
switch( ensembleCase ){ |
1286 |
+ |
|
1287 |
+ |
case NVE_ENS: |
1288 |
+ |
new NVE( info, the_ff ); |
1289 |
+ |
break; |
1290 |
+ |
|
1291 |
+ |
case NVT_ENS: |
1292 |
+ |
myNVT = new NVT( info, the_ff ); |
1293 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1294 |
+ |
|
1295 |
+ |
if (globals->haveTauThermostat()) |
1296 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1297 |
+ |
|
1298 |
+ |
else { |
1299 |
+ |
sprintf( painCave.errMsg, |
1300 |
+ |
"SimSetup error: If you use the NVT\n" |
1301 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1302 |
+ |
painCave.isFatal = 1; |
1303 |
+ |
simError(); |
1304 |
+ |
} |
1305 |
+ |
break; |
1306 |
+ |
|
1307 |
+ |
case NPTi_ENS: |
1308 |
+ |
myNPTi = new NPTi( info, the_ff ); |
1309 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1310 |
+ |
|
1311 |
+ |
if (globals->haveTargetPressure()) |
1312 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1313 |
+ |
else { |
1314 |
+ |
sprintf( painCave.errMsg, |
1315 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1316 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1317 |
+ |
painCave.isFatal = 1; |
1318 |
+ |
simError(); |
1319 |
+ |
} |
1320 |
+ |
|
1321 |
+ |
if( globals->haveTauThermostat() ) |
1322 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1323 |
+ |
else{ |
1324 |
+ |
sprintf( painCave.errMsg, |
1325 |
+ |
"SimSetup error: If you use an NPT\n" |
1326 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1327 |
+ |
painCave.isFatal = 1; |
1328 |
+ |
simError(); |
1329 |
+ |
} |
1330 |
+ |
|
1331 |
+ |
if( globals->haveTauBarostat() ) |
1332 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1333 |
+ |
else{ |
1334 |
+ |
sprintf( painCave.errMsg, |
1335 |
+ |
"SimSetup error: If you use an NPT\n" |
1336 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1337 |
+ |
painCave.isFatal = 1; |
1338 |
+ |
simError(); |
1339 |
+ |
} |
1340 |
+ |
break; |
1341 |
+ |
|
1342 |
+ |
case NPTf_ENS: |
1343 |
+ |
myNPTf = new NPTf( info, the_ff ); |
1344 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1345 |
+ |
|
1346 |
+ |
if (globals->haveTargetPressure()) |
1347 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1348 |
+ |
else { |
1349 |
+ |
sprintf( painCave.errMsg, |
1350 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1351 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1352 |
+ |
painCave.isFatal = 1; |
1353 |
+ |
simError(); |
1354 |
+ |
} |
1355 |
+ |
|
1356 |
+ |
if( globals->haveTauThermostat() ) |
1357 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1358 |
+ |
else{ |
1359 |
+ |
sprintf( painCave.errMsg, |
1360 |
+ |
"SimSetup error: If you use an NPT\n" |
1361 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1362 |
+ |
painCave.isFatal = 1; |
1363 |
+ |
simError(); |
1364 |
+ |
} |
1365 |
+ |
|
1366 |
+ |
if( globals->haveTauBarostat() ) |
1367 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1368 |
+ |
else{ |
1369 |
+ |
sprintf( painCave.errMsg, |
1370 |
+ |
"SimSetup error: If you use an NPT\n" |
1371 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1372 |
+ |
painCave.isFatal = 1; |
1373 |
+ |
simError(); |
1374 |
+ |
} |
1375 |
+ |
break; |
1376 |
+ |
|
1377 |
+ |
case NPTim_ENS: |
1378 |
+ |
myNPTim = new NPTim( info, the_ff ); |
1379 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1380 |
+ |
|
1381 |
+ |
if (globals->haveTargetPressure()) |
1382 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1383 |
+ |
else { |
1384 |
+ |
sprintf( painCave.errMsg, |
1385 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1386 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1387 |
+ |
painCave.isFatal = 1; |
1388 |
+ |
simError(); |
1389 |
+ |
} |
1390 |
+ |
|
1391 |
+ |
if( globals->haveTauThermostat() ) |
1392 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1393 |
+ |
else{ |
1394 |
+ |
sprintf( painCave.errMsg, |
1395 |
+ |
"SimSetup error: If you use an NPT\n" |
1396 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1397 |
+ |
painCave.isFatal = 1; |
1398 |
+ |
simError(); |
1399 |
+ |
} |
1400 |
+ |
|
1401 |
+ |
if( globals->haveTauBarostat() ) |
1402 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1403 |
+ |
else{ |
1404 |
+ |
sprintf( painCave.errMsg, |
1405 |
+ |
"SimSetup error: If you use an NPT\n" |
1406 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1407 |
+ |
painCave.isFatal = 1; |
1408 |
+ |
simError(); |
1409 |
+ |
} |
1410 |
+ |
break; |
1411 |
+ |
|
1412 |
+ |
case NPTfm_ENS: |
1413 |
+ |
myNPTfm = new NPTfm( info, the_ff ); |
1414 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1415 |
+ |
|
1416 |
+ |
if (globals->haveTargetPressure()) |
1417 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1418 |
+ |
else { |
1419 |
+ |
sprintf( painCave.errMsg, |
1420 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1421 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1422 |
+ |
painCave.isFatal = 1; |
1423 |
+ |
simError(); |
1424 |
+ |
} |
1425 |
+ |
|
1426 |
+ |
if( globals->haveTauThermostat() ) |
1427 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1428 |
+ |
else{ |
1429 |
+ |
sprintf( painCave.errMsg, |
1430 |
+ |
"SimSetup error: If you use an NPT\n" |
1431 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1432 |
+ |
painCave.isFatal = 1; |
1433 |
+ |
simError(); |
1434 |
+ |
} |
1435 |
+ |
|
1436 |
+ |
if( globals->haveTauBarostat() ) |
1437 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1438 |
+ |
else{ |
1439 |
+ |
sprintf( painCave.errMsg, |
1440 |
+ |
"SimSetup error: If you use an NPT\n" |
1441 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1442 |
+ |
painCave.isFatal = 1; |
1443 |
+ |
simError(); |
1444 |
+ |
} |
1445 |
+ |
break; |
1446 |
+ |
|
1447 |
+ |
default: |
1448 |
+ |
sprintf( painCave.errMsg, |
1449 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1450 |
+ |
painCave.isFatal = 1; |
1451 |
+ |
simError(); |
1452 |
+ |
} |
1453 |
+ |
|
1454 |
+ |
} |
1455 |
+ |
|
1456 |
+ |
void SimSetup::initFortran( void ){ |
1457 |
+ |
|
1458 |
+ |
info->refreshSim(); |
1459 |
+ |
|
1460 |
+ |
if( !strcmp( info->mixingRule, "standard") ){ |
1461 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1462 |
+ |
} |
1463 |
+ |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1464 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1465 |
+ |
} |
1466 |
+ |
else{ |
1467 |
+ |
sprintf( painCave.errMsg, |
1468 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1469 |
+ |
info->mixingRule ); |
1470 |
+ |
painCave.isFatal = 1; |
1471 |
+ |
simError(); |
1472 |
+ |
} |
1473 |
+ |
|
1474 |
+ |
|
1475 |
+ |
#ifdef IS_MPI |
1476 |
+ |
strcpy( checkPointMsg, |
1477 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1478 |
+ |
MPIcheckPoint(); |
1479 |
+ |
#endif // is_mpi |
1480 |
+ |
|
1481 |
+ |
} |